UC Davis, USA, testimonial on Karyosoft's Variant Platform
1. What is your research?
My research has involved the discovery and characterization of natural and induced genetic variation in plants and animals.
2. What do you use variant data in your research for and how important they are?
Variant data is highly important for my research. The majority of my work has involved functional genomic studies where gene-variants are sought. In addition, I have used non-genic variants in population genetic studies.
3. How do you run variant analysis (discovery) currently?
Variant analysis is run either on a dedicated workstation or on a shared computer cluster. I primarily use GATK to call variants.
4. What are the pain points (hardest part) for variant discovery with your current process?
I would say that the computational time needed to complete an analysis pipeline (from raw data through annotated variants) is the biggest bottleneck. The second biggest would be the organization of the various intermediary files produced when running a analysis.
5. Why are these problems hard for you?
As soon as raw sequence data becomes available (e.g. fastq), there is often pressured to get the analysis done as soon as possible.
6. What have you done to circumvent those pain points?
When processing many samples, the data has sometimes been split and processed on different computers.
7. What don’t you like about the solutions that you have tried before using Karyosoft’s Variants platform?
Splitting an analysis on different computers requires more organization and therefore more time. Running an analysis on a cluster has also required splitting data into many small pieces to maximize performance, but this also creates extra work in terms of file/data management.
8. What was your experience using Karyosoft’s Variants platform?
I liked using the platform. The user interface is intuitive and graphical, making it easy to start an analysis. The software used for the analysis (e.g., GATK) matches my methods of choice and are industry standards. The platform allows modifications of various software parameters. This allowed me to run my analysis using the same conditions that I was previously using. It is no surprise, therefore, that I could produce high quality data that met my expectations based on my previous work. Further, when the analysis was done, I appreciated the graphical interface to select and download the various output files. This was easy to navigate, allowing me to quickly select the intermediary files that I wanted to retain (e.g., BAM alignments).
9. What values do you think the Karyosoft's Variants platform brings to your research?
Because I was previously using the same GATK, the big improvement to me is the fact that the analysis is very fast (complete in hours versus days), and the fact that the output files are organized and easy to access, allowing me to quickly save only the intermediary files I deem important. While on a detailed level I am familiar with the GATK, I think the platform is an excellent choice for those without extensive experience with command line tools.
10. Do you recommend the Karyosoft's Variants platform to fellow researchers?
Yes, I think both those new to the field and the experienced research can benefit from using the platform. The data and various analyses (annotation) are exactly what I want/expect.